Mon Oct 10 17:15:21 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:15:21 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5519380 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -28.38600 36.11400 ymin,ymax (A): -24.58400 23.64900 zmin,zma (A): -37.91700 9.094000 x,y,z range (A): 64.50000 48.23300 47.01100 scale (grids/A): 0.5519380 object centre (A): 3.864001 -0.4674997 -14.41150 number of atom coordinates read : 3020 total number of charged atoms : 2878 net assigned charge : -3.471966 assigned positive charge : 457.9069 centred at (gu) : 90.17782 90.06680 90.54208 assigned negative charge : -461.3801 centred at (gu) : 90.22953 90.18961 90.66772 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5935 nv = 96 ne = 84 npr = 60162 no. pairs analyzed = 60162 no. exposed pairs = 4062 no. arc points = 28532 no. surface atoms = 1363 nbur = 1657 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 241 mr = 2899 m= 0 mr = 4 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 number of dielectric boundary points 3273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2882 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9870998E-10 -1.5559816E-09 midg,1,midg; midg,igrid,midg 7.6461482E-10 -1.3574915E-09 1,midg,midg; igrid,midg,midg 1.7097383E-10 -7.4189971E-10 gauss-seidel spectral radius is 0.9830805 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 17:15:22 rms-change max change #iterations 7.8488983E-02 11.83978 at 10iterations 5.2812919E-03 0.8090048 at 20iterations 3.5988391E-04 5.8239937E-02 at 30iterations 2.4298386E-05 3.8394928E-03 at 40iterations 1.7826455E-06 2.5749207E-04 at 50iterations finished qdiffx linear iterations at : 17:15:25 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 1.7826455E-06 2.5749207E-04 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 17:15:25 3.246u 0.176s 0:03.85 88.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:15:25 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.655814 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -28.38600 36.11400 ymin,ymax (A): -24.58400 23.64900 zmin,zma (A): -37.91700 9.094000 x,y,z range (A): 64.50000 48.23300 47.01100 scale (grids/A): 1.655814 object centre (A): 3.864001 -0.4674997 -14.41150 number of atom coordinates read : 3020 total number of charged atoms : 2878 net assigned charge : -3.471966 assigned positive charge : 457.9069 centred at (gu) : 90.53300 90.19968 91.62572 assigned negative charge : -461.3801 centred at (gu) : 90.68826 90.56850 92.00256 start vw surface at 0.2300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 66159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28532 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19530 mr = 43514 m= 1943 mr = 12757 m= 59 mr = 841 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 0.5400000 number of dielectric boundary points 30573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 334 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 22154 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5519380 object centre at (A) : 3.864001 -0.4674997 -14.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7924480E-03 -6.9364528E-03 midg,1,midg; midg,igrid,midg 6.0993307E-03 -1.7725743E-02 1,midg,midg; igrid,midg,midg 8.3391566E-04 -1.6802562E-02 gauss-seidel spectral radius is 0.9982463 estimated iterations to convergence 190 setup time was (sec) 0.8100000 now iterating at: 17:15:26 rms-change max change #iterations 3.478323 145.7139 at 10iterations 1.459574 57.87086 at 20iterations 0.6183516 23.85479 at 30iterations 0.2602489 9.627767 at 40iterations 0.1102557 3.818529 at 50iterations 4.6739303E-02 1.666945 at 60iterations 1.9656053E-02 0.7853909 at 70iterations 8.3313296E-03 0.3064890 at 80iterations 3.5181537E-03 0.1252441 at 90iterations 1.4918711E-03 4.8980713E-02 at 100iterations 6.2908058E-04 2.2686005E-02 at 110iterations 2.6664193E-04 9.6511841E-03 at 120iterations finished qdiffx linear iterations at : 17:15:32 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 2.6664193E-04 9.6511841E-03 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 17:15:33 6.971u 0.170s 0:07.44 95.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:15:33 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.483721 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -28.38600 36.11400 ymin,ymax (A): -24.58400 23.64900 zmin,zma (A): -37.91700 9.094000 x,y,z range (A): 64.50000 48.23300 47.01100 scale (grids/A): 2.483721 object centre (A): 3.864001 -0.4674997 -14.41150 number of atom coordinates read : 3020 total number of charged atoms : 2878 net assigned charge : -3.471966 assigned positive charge : 457.9069 centred at (gu) : 90.79925 90.29946 92.43843 assigned negative charge : -461.3801 centred at (gu) : 91.03238 90.85284 93.00380 start vw surface at 0.2200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 153766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28532 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67929 mr = 107120 m= 18512 mr = 52087 m= 2970 mr = 13481 m= 226 mr = 1813 m= 3 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 498 time to turn everything in is 1.160000 number of dielectric boundary points 68806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 22998 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.655814 object centre at (A) : 3.864001 -0.4674997 -14.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5068069E-02 -5.9700284E-02 midg,1,midg; midg,igrid,midg 0.1059883 -0.2484974 1,midg,midg; igrid,midg,midg 6.0109306E-02 -0.3328347 gauss-seidel spectral radius is 0.9991654 estimated iterations to convergence 273 setup time was (sec) 1.430000 now iterating at: 17:15:34 rms-change max change #iterations 9.071776 288.4825 at 10iterations 5.127058 137.7202 at 20iterations 2.884946 66.87587 at 30iterations 1.619881 36.83411 at 40iterations 0.9033418 18.70302 at 50iterations 0.5056891 13.79765 at 60iterations 0.2812746 6.124690 at 70iterations 0.1561906 3.620728 at 80iterations 8.6918682E-02 2.333946 at 90iterations 4.8205204E-02 1.212137 at 100iterations 2.6751701E-02 0.5840601 at 110iterations 1.4848946E-02 0.3109941 at 120iterations 8.2250647E-03 0.1616421 at 130iterations 4.5702555E-03 9.0369225E-02 at 140iterations 2.5294321E-03 5.5950165E-02 at 150iterations 1.4034865E-03 3.0731201E-02 at 160iterations 7.7806268E-04 1.5996933E-02 at 170iterations 4.3087322E-04 8.5926056E-03 at 180iterations finished qdiffx linear iterations at : 17:15:44 total time elapsed so far: 10.98000 # loops : 180 mean,max change (kT/e) : 4.3087322E-04 8.5926056E-03 energy calculations done at 10.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 17:15:44 11.154u 0.202s 0:11.71 96.9% 0+0k 0+0io 0pf+0w